Google charged my account more than the amount required to pay.

There is nothing to file as this is normal. AdWords is not going to run $3.01 payments when they are due, the system is going to allow you to start advertising with or without a pre-payment (conditions vary), and then 30 days after you start, your billing cycle renews and a payment will pull from your payment source. The $50 is now a credit you will work off. The money you paid is not lost, you did not overpay... it was paid towards your account for future charges.

Now that the $50 is there for use, in another 30 days when the bill cycle renews again (it will every 30 days for life), you will not be charged the $50, if you do not use your credit up before then. The system will simply use that $50 until it is gone and then it will run another $50 payment and apply it as a credit again.

You can learn more about your billing by opening Google AdWords, clicking on the gear icon (or stacked dots) in the upper right hand corner and clicking on Billing. You will see a payment dashboard with charts of data that show details.

Please read the information in this link to expand your understanding. There are links along the right side of the page, and at the bottom, too... which you should read all of them.